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@@ -535,7 +535,13 @@ class ReachGraspIO(BlackrockIO):
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for signalname in ['GripForceSignals', 'DisplacementSignal']:
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for analog_events in trial_sec['AnalogEvents'][signalname].properties:
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+ # skip invalid values
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+ if analog_events.values == [-1]: # this was used as default time
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+ continue
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+
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time = analog_events.values * pq.CompoundUnit(analog_events.unit)
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+ time = time.rescale('ms')
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+
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if time >= t_start and time < t_stop:
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event_name.append(analog_events.name)
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event_time.append(time)
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@@ -546,9 +552,7 @@ class ReachGraspIO(BlackrockIO):
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# Create event object with analog events
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analog_events = neo.Event(
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- times=pq.Quantity(
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- [_.magnitude for _ in event_time],
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- units=event_time[0].units).rescale('ms').flatten(),
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+ times=pq.Quantity(event_time, 'ms').flatten(),
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labels=np.array(event_name),
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name='AnalogTrialEvents',
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description='Events extracted from analog signals')
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@@ -579,16 +583,18 @@ class ReachGraspIO(BlackrockIO):
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events.name = "DigitalTrialEvents"
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events.description = "Trial " + events.description.lower()
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+ events_rescaled = events.rescale(pq.CompoundUnit('1/30000*s'))
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+
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# Extract beginning of first complete trial
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tson_label = self.event_labels_codes['TS-ON'][0]
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- if tson_label in events.labels:
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- first_TSon_idx = list(events.labels).index(tson_label)
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+ if tson_label in events_rescaled.labels:
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+ first_TSon_idx = list(events_rescaled.labels).index(tson_label)
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else:
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- first_TSon_idx = len(events.labels)
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+ first_TSon_idx = len(events_rescaled.labels)
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# Extract end of last complete trial
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stop_label = self.event_labels_codes['STOP'][0]
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- if stop_label in events.labels:
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- last_WSoff_idx = len(events.labels) - list(events.labels[::-1]).index(stop_label) - 1
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+ if stop_label in events_rescaled.labels:
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+ last_WSoff_idx = len(events_rescaled.labels) - list(events_rescaled.labels[::-1]).index(stop_label) - 1
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else:
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last_WSoff_idx = -1
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@@ -598,7 +604,7 @@ class ReachGraspIO(BlackrockIO):
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trial_timestamp_ID = []
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trialtypes = {-1: 'NONE'}
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trialsequence = {-1: 0}
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- for i, l in enumerate(events.labels):
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+ for i, l in enumerate(events_rescaled.labels):
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if i < first_TSon_idx or i > last_WSoff_idx:
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trial_event_labels.append('NONE')
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trial_ID.append(-1)
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@@ -607,9 +613,9 @@ class ReachGraspIO(BlackrockIO):
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# interpretation of TS-ON
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if self.event_labels_str[l] == 'TS-ON':
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if i > 0:
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- prev_ev = events.labels[i - 1]
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+ prev_ev = events_rescaled.labels[i - 1]
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if self.event_labels_str[prev_ev] in ['STOP', 'TS-OFF/STOP']:
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- timestamp_id = int(events.times[i].item())
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+ timestamp_id = int(round(events_rescaled.times[i].item()))
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trial_timestamp_ID.append(timestamp_id)
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trial_event_labels.append('TS-ON')
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trialsequence[timestamp_id] = self.__set_bit(
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@@ -619,7 +625,7 @@ class ReachGraspIO(BlackrockIO):
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trial_timestamp_ID.append(timestamp_id)
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trial_event_labels.append('TS-ON-ERROR')
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else:
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- timestamp_id = int(events.times[i].item())
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+ timestamp_id = int(events_rescaled.times[i].item())
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trial_timestamp_ID.append(timestamp_id)
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trial_event_labels.append('TS-ON')
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trialsequence[timestamp_id] = self.__set_bit(
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@@ -654,7 +660,7 @@ class ReachGraspIO(BlackrockIO):
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elif self.event_labels_str[l] == 'TS-OFF/STOP':
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trial_timestamp_ID.append(timestamp_id)
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trial_ID.append(ID)
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- prev_ev = events.labels[i - 1]
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+ prev_ev = events_rescaled.labels[i - 1]
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if self.event_labels_str[prev_ev] == 'TS-ON':
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trial_event_labels.append('TS-OFF')
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elif prev_ev in self.event_labels_codes['ERROR-FLASH-ON']:
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@@ -671,7 +677,7 @@ class ReachGraspIO(BlackrockIO):
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elif self.event_labels_str[l] == 'WS-ON/CUE-OFF':
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trial_timestamp_ID.append(timestamp_id)
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trial_ID.append(ID)
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- prev_ev = events.labels[i - 1]
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+ prev_ev = events_rescaled.labels[i - 1]
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if self.event_labels_str[prev_ev] in ['TS-ON', 'TS-OFF/STOP']:
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trial_event_labels.append('WS-ON')
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trialsequence[timestamp_id] = self.__set_bit(
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@@ -689,7 +695,7 @@ class ReachGraspIO(BlackrockIO):
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elif l in self.event_labels_codes['CUE/GO']:
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trial_timestamp_ID.append(timestamp_id)
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trial_ID.append(ID)
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- prprev_ev = events.labels[i - 2]
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+ prprev_ev = events_rescaled.labels[i - 2]
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if self.event_labels_str[prprev_ev] in ['TS-ON', 'TS-OFF/STOP']:
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trial_event_labels.append('CUE-ON')
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trialsequence[timestamp_id] = self.__set_bit(
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@@ -708,7 +714,7 @@ class ReachGraspIO(BlackrockIO):
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elif self.event_labels_str[l] == 'STOP':
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trial_timestamp_ID.append(timestamp_id)
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trial_ID.append(ID)
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- prev_ev = self.event_labels_str[events.labels[i - 1]]
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+ prev_ev = self.event_labels_str[events_rescaled.labels[i - 1]]
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if prev_ev == 'ERROR-FLASH-ON':
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trial_event_labels.append('ERROR-FLASH-OFF')
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else:
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@@ -720,7 +726,7 @@ class ReachGraspIO(BlackrockIO):
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elif l in self.event_labels_codes['SR']:
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trial_timestamp_ID.append(timestamp_id)
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trial_ID.append(ID)
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- prev_ev = events.labels[i - 1]
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+ prev_ev = events_rescaled.labels[i - 1]
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if prev_ev in self.event_labels_codes['SR']:
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trial_event_labels.append('SR-REP')
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elif prev_ev in self.event_labels_codes['RW-ON']:
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@@ -730,11 +736,11 @@ class ReachGraspIO(BlackrockIO):
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trialsequence[timestamp_id] = self.__set_bit(
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trialsequence[timestamp_id],
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self.trial_const_sequence_codes['SR'])
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- # interpretation of RW events
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+ # interpretation of RW events_rescaled
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elif l in self.event_labels_codes['RW-ON']:
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trial_timestamp_ID.append(timestamp_id)
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trial_ID.append(ID)
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- prev_ev = events.labels[i - 1]
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+ prev_ev = events_rescaled.labels[i - 1]
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if prev_ev in self.event_labels_codes['RW-ON']:
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trial_event_labels.append('RW-ON-REP')
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else:
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@@ -1062,7 +1068,7 @@ class ReachGraspIO(BlackrockIO):
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if event.name in ['AnalogTrialEvents', 'DigitalTrialEvents']:
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# Extract event times
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if event_time is None:
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- event_time = event.times.magnitude
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+ event_time = event.times.magnitude.flatten()
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event_units = event.times.units
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else:
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event_time = np.concatenate((
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@@ -1459,7 +1465,7 @@ class ReachGraspIO(BlackrockIO):
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Event annotations:
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The resulting Block contains three Event objects with the
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following names:
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- "DigitalTrialEvents' contains all digitally recorded events
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+ 'DigitalTrialEvents' contains all digitally recorded events
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returned by BlackrockIO, annotated with semantic labels
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in accordance with the reach-to-grasp experiment (e.g.,
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'TS-ON').
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@@ -1671,6 +1677,7 @@ class ReachGraspIO(BlackrockIO):
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for st in seg.spiketrains:
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self.__annotate_electrode_rejections(st)
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+
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for ev in seg.events:
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# Modify digital trial events to include semantic event information
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if ev.name == 'digital_input_port':
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